Workshops Teach Computational Skills Needed to Advance Research


By Tatiana Tomich, BIO5 Institute, and Shelley Littin, iPlant Collaborative

To advance science today, researchers must not only be experts in their field, but must also be able to use computing to analyze, interpret, and share data. Since most scientists were not formally trained in computational processes, they must learn the skills necessary to quickly, efficiently, and reliably process datasets and analyses.

In answer to this need, the University of Arizona’s BIO5 Institute and iPlant Collaborative have teamed up to host a series of Software Carpentry workshops, offering instruction to researchers, students, and educators across the state that will allow them to hone their computing skills. At the same time, these organizations are aiming to increase the number of trainers able to provide instruction in managing big data.

Uwe Hilgert, PhD, and Director of STEM Training for BIO5 and iPlant, envisioned these workshops as an opportunity to “bring together already existing computational strengths and collaborations at UA.” Hilgert has seen firsthand how important it is that researchers be empowered with the ability to utilize big data to further scientific goals.

The first workshop was held in February 2015, and proved to be a huge success. The two-day session filled within 36 hours of opening registration, with over 50 attendees hailing from all three of Arizona’s public universities, and a wide range of disciplines including biosciences, management information systems, computer sciences, engineering, physics, and statistics.

According to Hilgert, “We saw early on that the need for these skills transcends biologists, and transcends the UA.” Following the success of the inaugural workshop, two more sessions were subsequently held at Arizona State University.

The latest workshop was held at UA on October 3-4th with 94 registered participants. “The fact that demand continues to exceed available capacity clearly shows that there is a strong need for this kind of training,” said Hilgert.

In addition, several previous workshop attendees from UA’s School of Plant Sciences and from iPlant served as co-instructors of the latest session. This fulfills another goal of the training program: to increase the number of instructors that are not only able to teach Software- and Data- Carpentry workshops, but who will also use iPlant cyberinfrastructure and other UA computing tools to do so.

Cutting-edge software and infrastructure support for complex data sequencing and cloud computing developed by iPlant and University Information Technology Services (UITS) is used extensively in the training.

“We want the attendees to walk away with a sense of how different software-related technologies can, and do, fit together,” said Jonathan Strootman, an iPlant software developer and co-instructor of the workshop. “We can't teach them everything we know in two days, but we can remove enough of the mystery to help them get started.”

Attendees were led through basic programming and data management skills, and were trained to work with the software that will allow them to efficiently handle large data sets.

“This training has better positioned me to make full use of R-programming and the iPlant cloud to better manage my data, analyses, and figures to deliver higher impact science in tree ring research,” noted Paul Szejner of the UA’s laboratory of tree ring research, a workshop participant.

Without the need to outsource, researchers are given more control over their work, the interpretation of their findings, and how to better share this to maximize collaborative impact. These skills were not traditionally needed for researchers, however as science moves fully into the digital age, knowing how to handle data and computational analyses becomes imperative.

The software carpentry workshop was also supported by the Arizona Environmental Grid Infrastructure Service (AEGIS), a statewide Arizona initiative to provision the transition to informatics-intensive research programs, funded by a Regents’ Innovation Award to the UA, ASU and NAU.

Founded in 1998, Software Carpentry hosts brief, intensive workshops geared toward researchers in science, engineering, medicine, and related fields, and covering skills including program design, version control, testing, and task automation.